Multiple sequence alignment - TraesCS7B01G175200

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7B01G175200 chr7B 100.000 2582 0 0 961 3542 246387457 246384876 0.000000e+00 4769.0
1 TraesCS7B01G175200 chr7B 100.000 623 0 0 1 623 246388417 246387795 0.000000e+00 1151.0
2 TraesCS7B01G175200 chr7B 97.323 523 14 0 3020 3542 698922460 698922982 0.000000e+00 889.0
3 TraesCS7B01G175200 chr7B 86.420 81 10 1 1 80 34848040 34847960 1.750000e-13 87.9
4 TraesCS7B01G175200 chr7B 95.122 41 2 0 104 144 44763775 44763735 8.210000e-07 65.8
5 TraesCS7B01G175200 chr7B 88.889 54 4 2 30 82 396718592 396718644 8.210000e-07 65.8
6 TraesCS7B01G175200 chr7D 95.126 1785 64 10 1023 2789 266207226 266209005 0.000000e+00 2793.0
7 TraesCS7B01G175200 chr7D 90.431 418 22 9 188 603 266206647 266207048 5.200000e-148 534.0
8 TraesCS7B01G175200 chr7D 81.609 174 25 6 2620 2788 266210051 266210222 1.710000e-28 137.0
9 TraesCS7B01G175200 chr7D 82.609 92 13 3 1 92 265079694 265079782 1.050000e-10 78.7
10 TraesCS7B01G175200 chr7D 97.561 41 1 0 104 144 107509776 107509816 1.760000e-08 71.3
11 TraesCS7B01G175200 chr7D 84.507 71 9 2 2228 2297 511663577 511663646 6.340000e-08 69.4
12 TraesCS7B01G175200 chr7D 95.238 42 2 0 104 145 628611958 628611999 2.280000e-07 67.6
13 TraesCS7B01G175200 chr7D 88.462 52 5 1 2246 2296 511689104 511689155 1.060000e-05 62.1
14 TraesCS7B01G175200 chr7A 96.653 1255 29 2 1428 2669 291659825 291661079 0.000000e+00 2073.0
15 TraesCS7B01G175200 chr7A 95.418 371 17 0 1023 1393 291659456 291659826 3.040000e-165 592.0
16 TraesCS7B01G175200 chr7A 87.697 317 22 6 288 603 291658999 291659299 1.560000e-93 353.0
17 TraesCS7B01G175200 chr7A 93.750 96 6 0 2850 2945 291663054 291663149 1.020000e-30 145.0
18 TraesCS7B01G175200 chr6D 80.608 1382 233 26 1163 2518 157452019 157450647 0.000000e+00 1035.0
19 TraesCS7B01G175200 chr6D 84.375 96 14 1 1 96 47670359 47670265 3.760000e-15 93.5
20 TraesCS7B01G175200 chr1B 97.333 525 12 1 3020 3542 61991903 61991379 0.000000e+00 891.0
21 TraesCS7B01G175200 chr1B 97.505 521 13 0 3022 3542 672156982 672156462 0.000000e+00 891.0
22 TraesCS7B01G175200 chr1B 77.214 1400 257 39 1164 2518 616771091 616769709 0.000000e+00 761.0
23 TraesCS7B01G175200 chr2B 96.964 527 14 1 3018 3542 752930243 752930769 0.000000e+00 883.0
24 TraesCS7B01G175200 chr2B 96.941 523 14 1 3022 3542 617150127 617149605 0.000000e+00 876.0
25 TraesCS7B01G175200 chr2B 96.388 526 16 2 3019 3542 779284372 779283848 0.000000e+00 863.0
26 TraesCS7B01G175200 chr2B 95.872 533 19 2 3013 3542 369807462 369806930 0.000000e+00 859.0
27 TraesCS7B01G175200 chr2B 92.683 82 6 0 152 233 733462139 733462220 6.210000e-23 119.0
28 TraesCS7B01G175200 chr3B 97.132 523 13 1 3022 3542 671136192 671136714 0.000000e+00 881.0
29 TraesCS7B01G175200 chr3B 86.207 87 12 0 152 238 344651304 344651390 1.050000e-15 95.3
30 TraesCS7B01G175200 chr6B 96.941 523 14 1 3022 3542 704691640 704691118 0.000000e+00 876.0
31 TraesCS7B01G175200 chr6B 84.768 453 67 2 2067 2518 280999233 280998782 1.500000e-123 453.0
32 TraesCS7B01G175200 chr6B 76.028 851 168 22 1610 2445 20433597 20434426 3.290000e-110 409.0
33 TraesCS7B01G175200 chr6B 79.318 469 83 11 1163 1621 281005799 281005335 2.050000e-82 316.0
34 TraesCS7B01G175200 chr6B 82.609 92 15 1 1 91 8101188 8101279 2.930000e-11 80.5
35 TraesCS7B01G175200 chr6B 82.143 84 14 1 9 91 91077113 91077030 1.760000e-08 71.3
36 TraesCS7B01G175200 chr6B 93.333 45 3 0 101 145 682327016 682327060 2.280000e-07 67.6
37 TraesCS7B01G175200 chr1D 77.969 1398 253 36 1162 2518 450143753 450142370 0.000000e+00 824.0
38 TraesCS7B01G175200 chr1D 85.714 77 10 1 27 102 327720616 327720540 2.930000e-11 80.5
39 TraesCS7B01G175200 chr1D 97.619 42 1 0 104 145 290702836 290702795 4.900000e-09 73.1
40 TraesCS7B01G175200 chr1A 77.937 1396 257 30 1162 2518 545418581 545417198 0.000000e+00 824.0
41 TraesCS7B01G175200 chr1A 86.420 81 10 1 153 233 347909029 347909108 1.750000e-13 87.9
42 TraesCS7B01G175200 chr5B 83.696 92 14 1 1 91 493162256 493162347 6.300000e-13 86.1
43 TraesCS7B01G175200 chr4D 97.561 41 1 0 104 144 464078532 464078492 1.760000e-08 71.3
44 TraesCS7B01G175200 chr3D 83.333 78 11 2 1 77 465963857 465963933 1.760000e-08 71.3
45 TraesCS7B01G175200 chr3D 97.561 41 1 0 104 144 535976887 535976847 1.760000e-08 71.3
46 TraesCS7B01G175200 chr2D 97.561 41 1 0 104 144 121699888 121699848 1.760000e-08 71.3
47 TraesCS7B01G175200 chr4A 95.238 42 2 0 104 145 722343004 722343045 2.280000e-07 67.6


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G175200 chr7B 246384876 246388417 3541 True 2960.000000 4769 100.000000 1 3542 2 chr7B.!!$R3 3541
1 TraesCS7B01G175200 chr7B 698922460 698922982 522 False 889.000000 889 97.323000 3020 3542 1 chr7B.!!$F2 522
2 TraesCS7B01G175200 chr7D 266206647 266210222 3575 False 1154.666667 2793 89.055333 188 2789 3 chr7D.!!$F6 2601
3 TraesCS7B01G175200 chr7A 291658999 291663149 4150 False 790.750000 2073 93.379500 288 2945 4 chr7A.!!$F1 2657
4 TraesCS7B01G175200 chr6D 157450647 157452019 1372 True 1035.000000 1035 80.608000 1163 2518 1 chr6D.!!$R2 1355
5 TraesCS7B01G175200 chr1B 61991379 61991903 524 True 891.000000 891 97.333000 3020 3542 1 chr1B.!!$R1 522
6 TraesCS7B01G175200 chr1B 672156462 672156982 520 True 891.000000 891 97.505000 3022 3542 1 chr1B.!!$R3 520
7 TraesCS7B01G175200 chr1B 616769709 616771091 1382 True 761.000000 761 77.214000 1164 2518 1 chr1B.!!$R2 1354
8 TraesCS7B01G175200 chr2B 752930243 752930769 526 False 883.000000 883 96.964000 3018 3542 1 chr2B.!!$F2 524
9 TraesCS7B01G175200 chr2B 617149605 617150127 522 True 876.000000 876 96.941000 3022 3542 1 chr2B.!!$R2 520
10 TraesCS7B01G175200 chr2B 779283848 779284372 524 True 863.000000 863 96.388000 3019 3542 1 chr2B.!!$R3 523
11 TraesCS7B01G175200 chr2B 369806930 369807462 532 True 859.000000 859 95.872000 3013 3542 1 chr2B.!!$R1 529
12 TraesCS7B01G175200 chr3B 671136192 671136714 522 False 881.000000 881 97.132000 3022 3542 1 chr3B.!!$F2 520
13 TraesCS7B01G175200 chr6B 704691118 704691640 522 True 876.000000 876 96.941000 3022 3542 1 chr6B.!!$R4 520
14 TraesCS7B01G175200 chr6B 20433597 20434426 829 False 409.000000 409 76.028000 1610 2445 1 chr6B.!!$F2 835
15 TraesCS7B01G175200 chr1D 450142370 450143753 1383 True 824.000000 824 77.969000 1162 2518 1 chr1D.!!$R3 1356
16 TraesCS7B01G175200 chr1A 545417198 545418581 1383 True 824.000000 824 77.937000 1162 2518 1 chr1A.!!$R1 1356

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
121 122 0.101939 GTCCAGATACGAACCGGGAC 59.898 60.0 6.32 0.0 38.15 4.46 F
528 541 0.104120 CACACGACCACTTCTCCACA 59.896 55.0 0.00 0.0 0.00 4.17 F
611 624 0.388649 CCTTTGTCGACTCCCTCACG 60.389 60.0 17.92 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1185 1240 0.737715 CGAACTTGGCGAGGAAGAGG 60.738 60.00 6.71 0.0 0.00 3.69 R
2518 2644 0.735471 CTTCTGGAGACGATGAGCGA 59.265 55.00 0.00 0.0 44.57 4.93 R
2556 2682 4.769688 TCATATGTCGAGAGGTTGCATTT 58.230 39.13 1.90 0.0 0.00 2.32 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 4.112341 GTACACGACGCCGCCTCT 62.112 66.667 0.00 0.00 39.95 3.69
28 29 3.367743 TACACGACGCCGCCTCTT 61.368 61.111 0.00 0.00 39.95 2.85
29 30 3.332493 TACACGACGCCGCCTCTTC 62.332 63.158 0.00 0.00 39.95 2.87
39 40 4.400961 GCCTCTTCCTGCGTGCCT 62.401 66.667 0.00 0.00 0.00 4.75
40 41 2.435586 CCTCTTCCTGCGTGCCTG 60.436 66.667 0.00 0.00 0.00 4.85
41 42 2.345244 CTCTTCCTGCGTGCCTGT 59.655 61.111 0.00 0.00 0.00 4.00
42 43 2.031012 TCTTCCTGCGTGCCTGTG 59.969 61.111 0.00 0.00 0.00 3.66
43 44 3.730761 CTTCCTGCGTGCCTGTGC 61.731 66.667 0.00 0.00 38.26 4.57
44 45 4.254709 TTCCTGCGTGCCTGTGCT 62.255 61.111 0.00 0.00 38.71 4.40
45 46 2.786539 CTTCCTGCGTGCCTGTGCTA 62.787 60.000 0.00 0.00 38.71 3.49
46 47 2.124983 CCTGCGTGCCTGTGCTAT 60.125 61.111 0.00 0.00 38.71 2.97
47 48 1.746615 CCTGCGTGCCTGTGCTATT 60.747 57.895 0.00 0.00 38.71 1.73
48 49 0.461870 CCTGCGTGCCTGTGCTATTA 60.462 55.000 0.00 0.00 38.71 0.98
49 50 1.586422 CTGCGTGCCTGTGCTATTAT 58.414 50.000 0.00 0.00 38.71 1.28
50 51 1.262417 CTGCGTGCCTGTGCTATTATG 59.738 52.381 0.00 0.00 38.71 1.90
51 52 1.299541 GCGTGCCTGTGCTATTATGT 58.700 50.000 0.00 0.00 38.71 2.29
52 53 1.670811 GCGTGCCTGTGCTATTATGTT 59.329 47.619 0.00 0.00 38.71 2.71
53 54 2.539547 GCGTGCCTGTGCTATTATGTTG 60.540 50.000 0.00 0.00 38.71 3.33
54 55 2.677836 CGTGCCTGTGCTATTATGTTGT 59.322 45.455 0.00 0.00 38.71 3.32
55 56 3.242413 CGTGCCTGTGCTATTATGTTGTC 60.242 47.826 0.00 0.00 38.71 3.18
56 57 3.689161 GTGCCTGTGCTATTATGTTGTCA 59.311 43.478 0.00 0.00 38.71 3.58
57 58 4.336433 GTGCCTGTGCTATTATGTTGTCAT 59.664 41.667 0.00 0.00 38.71 3.06
58 59 5.527214 GTGCCTGTGCTATTATGTTGTCATA 59.473 40.000 0.00 0.00 38.71 2.15
59 60 5.759763 TGCCTGTGCTATTATGTTGTCATAG 59.240 40.000 0.00 0.00 36.84 2.23
60 61 5.180117 GCCTGTGCTATTATGTTGTCATAGG 59.820 44.000 0.00 0.00 36.37 2.57
61 62 6.291377 CCTGTGCTATTATGTTGTCATAGGT 58.709 40.000 0.00 0.00 37.75 3.08
62 63 6.767902 CCTGTGCTATTATGTTGTCATAGGTT 59.232 38.462 0.00 0.00 37.75 3.50
63 64 7.931407 CCTGTGCTATTATGTTGTCATAGGTTA 59.069 37.037 0.00 0.00 37.75 2.85
64 65 8.657074 TGTGCTATTATGTTGTCATAGGTTAC 57.343 34.615 0.00 0.00 37.75 2.50
65 66 8.261522 TGTGCTATTATGTTGTCATAGGTTACA 58.738 33.333 0.00 0.00 37.75 2.41
66 67 8.548721 GTGCTATTATGTTGTCATAGGTTACAC 58.451 37.037 0.00 0.00 37.75 2.90
67 68 8.261522 TGCTATTATGTTGTCATAGGTTACACA 58.738 33.333 0.00 0.00 37.75 3.72
68 69 8.765219 GCTATTATGTTGTCATAGGTTACACAG 58.235 37.037 0.00 0.00 37.75 3.66
69 70 9.817809 CTATTATGTTGTCATAGGTTACACAGT 57.182 33.333 0.00 0.00 37.75 3.55
70 71 7.899178 TTATGTTGTCATAGGTTACACAGTG 57.101 36.000 0.00 0.00 37.75 3.66
71 72 5.284861 TGTTGTCATAGGTTACACAGTGT 57.715 39.130 11.87 11.87 0.00 3.55
72 73 6.408107 TGTTGTCATAGGTTACACAGTGTA 57.592 37.500 9.51 9.51 0.00 2.90
73 74 6.999950 TGTTGTCATAGGTTACACAGTGTAT 58.000 36.000 14.34 2.52 32.20 2.29
74 75 7.094631 TGTTGTCATAGGTTACACAGTGTATC 58.905 38.462 14.34 12.98 32.20 2.24
75 76 7.039293 TGTTGTCATAGGTTACACAGTGTATCT 60.039 37.037 14.34 15.72 32.20 1.98
76 77 8.464404 GTTGTCATAGGTTACACAGTGTATCTA 58.536 37.037 14.34 17.12 32.20 1.98
77 78 7.993101 TGTCATAGGTTACACAGTGTATCTAC 58.007 38.462 14.34 9.51 32.20 2.59
78 79 7.067859 TGTCATAGGTTACACAGTGTATCTACC 59.932 40.741 19.54 19.54 33.54 3.18
79 80 6.548622 TCATAGGTTACACAGTGTATCTACCC 59.451 42.308 22.02 13.91 33.73 3.69
80 81 4.944177 AGGTTACACAGTGTATCTACCCT 58.056 43.478 22.02 15.39 33.73 4.34
81 82 4.954826 AGGTTACACAGTGTATCTACCCTC 59.045 45.833 22.02 7.17 33.73 4.30
82 83 4.954826 GGTTACACAGTGTATCTACCCTCT 59.045 45.833 17.48 0.00 32.20 3.69
83 84 5.067544 GGTTACACAGTGTATCTACCCTCTC 59.932 48.000 17.48 0.32 32.20 3.20
84 85 4.317530 ACACAGTGTATCTACCCTCTCA 57.682 45.455 3.69 0.00 0.00 3.27
85 86 4.673968 ACACAGTGTATCTACCCTCTCAA 58.326 43.478 3.69 0.00 0.00 3.02
86 87 5.273208 ACACAGTGTATCTACCCTCTCAAT 58.727 41.667 3.69 0.00 0.00 2.57
87 88 6.432581 ACACAGTGTATCTACCCTCTCAATA 58.567 40.000 3.69 0.00 0.00 1.90
88 89 7.069986 ACACAGTGTATCTACCCTCTCAATAT 58.930 38.462 3.69 0.00 0.00 1.28
89 90 8.225416 ACACAGTGTATCTACCCTCTCAATATA 58.775 37.037 3.69 0.00 0.00 0.86
90 91 9.249053 CACAGTGTATCTACCCTCTCAATATAT 57.751 37.037 0.00 0.00 0.00 0.86
102 103 9.327731 ACCCTCTCAATATATAAAAGACCTAGG 57.672 37.037 7.41 7.41 0.00 3.02
103 104 9.327731 CCCTCTCAATATATAAAAGACCTAGGT 57.672 37.037 16.26 16.26 0.00 3.08
106 107 9.892444 TCTCAATATATAAAAGACCTAGGTCCA 57.108 33.333 33.81 19.23 45.59 4.02
108 109 9.892444 TCAATATATAAAAGACCTAGGTCCAGA 57.108 33.333 33.81 19.41 45.59 3.86
112 113 6.651975 ATAAAAGACCTAGGTCCAGATACG 57.348 41.667 33.81 0.00 45.59 3.06
113 114 3.947612 AAGACCTAGGTCCAGATACGA 57.052 47.619 33.81 0.00 45.59 3.43
114 115 3.947612 AGACCTAGGTCCAGATACGAA 57.052 47.619 33.81 0.00 45.59 3.85
115 116 3.553904 AGACCTAGGTCCAGATACGAAC 58.446 50.000 33.81 9.32 45.59 3.95
116 117 2.622470 GACCTAGGTCCAGATACGAACC 59.378 54.545 28.87 1.58 39.08 3.62
117 118 1.607628 CCTAGGTCCAGATACGAACCG 59.392 57.143 0.00 0.00 36.87 4.44
118 119 1.607628 CTAGGTCCAGATACGAACCGG 59.392 57.143 0.00 0.00 36.87 5.28
119 120 1.041447 AGGTCCAGATACGAACCGGG 61.041 60.000 6.32 0.00 36.87 5.73
120 121 1.039233 GGTCCAGATACGAACCGGGA 61.039 60.000 6.32 0.00 0.00 5.14
121 122 0.101939 GTCCAGATACGAACCGGGAC 59.898 60.000 6.32 0.00 38.15 4.46
122 123 1.039233 TCCAGATACGAACCGGGACC 61.039 60.000 6.32 0.00 0.00 4.46
123 124 1.324740 CCAGATACGAACCGGGACCA 61.325 60.000 6.32 0.00 0.00 4.02
124 125 0.533491 CAGATACGAACCGGGACCAA 59.467 55.000 6.32 0.00 0.00 3.67
125 126 1.066716 CAGATACGAACCGGGACCAAA 60.067 52.381 6.32 0.00 0.00 3.28
126 127 1.206371 AGATACGAACCGGGACCAAAG 59.794 52.381 6.32 0.00 0.00 2.77
127 128 0.251073 ATACGAACCGGGACCAAAGG 59.749 55.000 6.32 0.00 0.00 3.11
128 129 1.829523 TACGAACCGGGACCAAAGGG 61.830 60.000 6.32 0.00 41.29 3.95
129 130 2.675423 GAACCGGGACCAAAGGGC 60.675 66.667 6.32 0.00 37.90 5.19
136 137 2.436824 GACCAAAGGGCCTCGCTC 60.437 66.667 6.46 0.00 37.90 5.03
137 138 3.978571 GACCAAAGGGCCTCGCTCC 62.979 68.421 6.46 0.00 37.90 4.70
138 139 3.721706 CCAAAGGGCCTCGCTCCT 61.722 66.667 6.46 0.00 32.23 3.69
139 140 2.437359 CAAAGGGCCTCGCTCCTG 60.437 66.667 6.46 0.00 31.54 3.86
140 141 3.721706 AAAGGGCCTCGCTCCTGG 61.722 66.667 6.46 0.00 31.54 4.45
150 151 3.453988 GCTCCTGGCGCTCTAGAT 58.546 61.111 7.64 0.00 0.00 1.98
151 152 1.006337 GCTCCTGGCGCTCTAGATG 60.006 63.158 7.64 1.69 0.00 2.90
152 153 1.459455 GCTCCTGGCGCTCTAGATGA 61.459 60.000 7.64 0.00 0.00 2.92
153 154 0.313672 CTCCTGGCGCTCTAGATGAC 59.686 60.000 7.64 0.00 0.00 3.06
154 155 0.106469 TCCTGGCGCTCTAGATGACT 60.106 55.000 7.64 0.00 0.00 3.41
155 156 0.313672 CCTGGCGCTCTAGATGACTC 59.686 60.000 7.64 0.00 0.00 3.36
156 157 0.313672 CTGGCGCTCTAGATGACTCC 59.686 60.000 7.64 0.00 0.00 3.85
157 158 0.395724 TGGCGCTCTAGATGACTCCA 60.396 55.000 7.64 0.00 0.00 3.86
158 159 0.965439 GGCGCTCTAGATGACTCCAT 59.035 55.000 7.64 0.00 35.29 3.41
159 160 2.163509 GGCGCTCTAGATGACTCCATA 58.836 52.381 7.64 0.00 32.09 2.74
160 161 2.757868 GGCGCTCTAGATGACTCCATAT 59.242 50.000 7.64 0.00 32.09 1.78
161 162 3.181491 GGCGCTCTAGATGACTCCATATC 60.181 52.174 7.64 0.00 32.09 1.63
162 163 3.441922 GCGCTCTAGATGACTCCATATCA 59.558 47.826 0.00 0.00 32.09 2.15
163 164 4.097741 GCGCTCTAGATGACTCCATATCAT 59.902 45.833 0.00 0.00 39.54 2.45
164 165 5.580661 CGCTCTAGATGACTCCATATCATG 58.419 45.833 0.00 0.00 36.92 3.07
165 166 5.125257 CGCTCTAGATGACTCCATATCATGT 59.875 44.000 0.00 0.00 36.92 3.21
166 167 6.563422 GCTCTAGATGACTCCATATCATGTC 58.437 44.000 0.00 0.00 36.92 3.06
167 168 6.377996 GCTCTAGATGACTCCATATCATGTCT 59.622 42.308 0.00 0.00 36.92 3.41
168 169 7.555914 GCTCTAGATGACTCCATATCATGTCTA 59.444 40.741 0.00 0.00 36.92 2.59
169 170 8.800370 TCTAGATGACTCCATATCATGTCTAC 57.200 38.462 0.00 0.00 36.92 2.59
170 171 8.386264 TCTAGATGACTCCATATCATGTCTACA 58.614 37.037 0.00 0.00 36.92 2.74
171 172 7.225784 AGATGACTCCATATCATGTCTACAC 57.774 40.000 0.00 0.00 36.92 2.90
172 173 6.779539 AGATGACTCCATATCATGTCTACACA 59.220 38.462 0.00 0.00 36.92 3.72
173 174 6.983906 TGACTCCATATCATGTCTACACAT 57.016 37.500 0.00 0.00 44.72 3.21
174 175 6.986250 TGACTCCATATCATGTCTACACATC 58.014 40.000 0.00 0.00 41.69 3.06
175 176 6.018589 ACTCCATATCATGTCTACACATCG 57.981 41.667 0.00 0.00 41.69 3.84
176 177 5.536538 ACTCCATATCATGTCTACACATCGT 59.463 40.000 0.00 0.00 41.69 3.73
177 178 6.715264 ACTCCATATCATGTCTACACATCGTA 59.285 38.462 0.00 0.00 41.69 3.43
178 179 6.909909 TCCATATCATGTCTACACATCGTAC 58.090 40.000 0.00 0.00 41.69 3.67
179 180 5.795441 CCATATCATGTCTACACATCGTACG 59.205 44.000 9.53 9.53 41.69 3.67
180 181 6.348213 CCATATCATGTCTACACATCGTACGA 60.348 42.308 21.93 21.93 41.69 3.43
181 182 4.531659 TCATGTCTACACATCGTACGAG 57.468 45.455 23.89 16.87 41.69 4.18
182 183 3.937079 TCATGTCTACACATCGTACGAGT 59.063 43.478 23.89 17.64 41.69 4.18
183 184 4.033702 TCATGTCTACACATCGTACGAGTC 59.966 45.833 23.89 7.12 41.69 3.36
184 185 2.674852 TGTCTACACATCGTACGAGTCC 59.325 50.000 23.89 8.35 0.00 3.85
185 186 2.674852 GTCTACACATCGTACGAGTCCA 59.325 50.000 23.89 6.65 0.00 4.02
186 187 3.125829 GTCTACACATCGTACGAGTCCAA 59.874 47.826 23.89 8.03 0.00 3.53
187 188 2.631418 ACACATCGTACGAGTCCAAG 57.369 50.000 23.89 11.82 0.00 3.61
188 189 1.884579 ACACATCGTACGAGTCCAAGT 59.115 47.619 23.89 12.42 0.00 3.16
189 190 2.095364 ACACATCGTACGAGTCCAAGTC 60.095 50.000 23.89 0.00 0.00 3.01
190 191 1.471684 ACATCGTACGAGTCCAAGTCC 59.528 52.381 23.89 0.00 0.00 3.85
191 192 1.471287 CATCGTACGAGTCCAAGTCCA 59.529 52.381 23.89 0.00 0.00 4.02
192 193 1.608055 TCGTACGAGTCCAAGTCCAA 58.392 50.000 15.28 0.00 0.00 3.53
203 204 6.388619 AGTCCAAGTCCAATTGTAACCTAT 57.611 37.500 4.43 0.00 0.00 2.57
204 205 6.415573 AGTCCAAGTCCAATTGTAACCTATC 58.584 40.000 4.43 0.00 0.00 2.08
206 207 6.884836 GTCCAAGTCCAATTGTAACCTATCTT 59.115 38.462 4.43 0.00 0.00 2.40
207 208 8.044908 GTCCAAGTCCAATTGTAACCTATCTTA 58.955 37.037 4.43 0.00 0.00 2.10
247 248 3.834489 ACTCTAGCAGATGATGGTTGG 57.166 47.619 0.00 0.00 40.89 3.77
250 251 3.106827 TCTAGCAGATGATGGTTGGACA 58.893 45.455 0.00 0.00 40.89 4.02
253 254 2.025605 AGCAGATGATGGTTGGACACAT 60.026 45.455 0.00 0.00 35.67 3.21
264 265 1.424403 TGGACACATCACTTAACGCG 58.576 50.000 3.53 3.53 0.00 6.01
281 282 0.588252 GCGCTCTCAGCTCACAAAAA 59.412 50.000 0.00 0.00 39.60 1.94
301 302 1.271856 TGACCCTTACGATGCTCCAA 58.728 50.000 0.00 0.00 0.00 3.53
307 308 2.354704 CCTTACGATGCTCCAACAAGGA 60.355 50.000 0.00 0.00 46.75 3.36
388 395 0.250338 GGTGTCCACTGGTTCTGGTC 60.250 60.000 0.00 0.00 0.00 4.02
393 400 1.679898 CACTGGTTCTGGTCCCTCC 59.320 63.158 0.00 0.00 0.00 4.30
394 401 1.127567 CACTGGTTCTGGTCCCTCCA 61.128 60.000 0.00 0.00 45.01 3.86
395 402 0.178861 ACTGGTTCTGGTCCCTCCAT 60.179 55.000 0.00 0.00 46.12 3.41
396 403 0.254178 CTGGTTCTGGTCCCTCCATG 59.746 60.000 0.00 0.00 46.12 3.66
431 444 2.329379 CAACTTTTCTCCTCCTCGTCG 58.671 52.381 0.00 0.00 0.00 5.12
432 445 1.618487 ACTTTTCTCCTCCTCGTCGT 58.382 50.000 0.00 0.00 0.00 4.34
434 447 1.540267 CTTTTCTCCTCCTCGTCGTCA 59.460 52.381 0.00 0.00 0.00 4.35
435 448 1.835494 TTTCTCCTCCTCGTCGTCAT 58.165 50.000 0.00 0.00 0.00 3.06
436 449 1.380524 TTCTCCTCCTCGTCGTCATC 58.619 55.000 0.00 0.00 0.00 2.92
437 450 0.252197 TCTCCTCCTCGTCGTCATCA 59.748 55.000 0.00 0.00 0.00 3.07
438 451 0.378962 CTCCTCCTCGTCGTCATCAC 59.621 60.000 0.00 0.00 0.00 3.06
439 452 1.030488 TCCTCCTCGTCGTCATCACC 61.030 60.000 0.00 0.00 0.00 4.02
440 453 1.032657 CCTCCTCGTCGTCATCACCT 61.033 60.000 0.00 0.00 0.00 4.00
441 454 0.378962 CTCCTCGTCGTCATCACCTC 59.621 60.000 0.00 0.00 0.00 3.85
442 455 1.062685 CCTCGTCGTCATCACCTCG 59.937 63.158 0.00 0.00 0.00 4.63
490 503 3.463505 CGTCTAGCAGCCACGTTG 58.536 61.111 0.00 0.00 0.00 4.10
491 504 2.730672 CGTCTAGCAGCCACGTTGC 61.731 63.158 2.86 2.86 40.00 4.17
492 505 2.432456 TCTAGCAGCCACGTTGCG 60.432 61.111 5.91 2.76 44.23 4.85
528 541 0.104120 CACACGACCACTTCTCCACA 59.896 55.000 0.00 0.00 0.00 4.17
560 573 0.813610 GCGTGCATATGTGGTAGCCA 60.814 55.000 4.29 0.00 0.00 4.75
603 616 1.341531 CCACTCACTCCTTTGTCGACT 59.658 52.381 17.92 0.00 0.00 4.18
604 617 2.608261 CCACTCACTCCTTTGTCGACTC 60.608 54.545 17.92 0.00 0.00 3.36
606 619 0.966920 TCACTCCTTTGTCGACTCCC 59.033 55.000 17.92 0.00 0.00 4.30
607 620 0.969894 CACTCCTTTGTCGACTCCCT 59.030 55.000 17.92 0.00 0.00 4.20
609 622 1.257743 CTCCTTTGTCGACTCCCTCA 58.742 55.000 17.92 0.00 0.00 3.86
610 623 0.966920 TCCTTTGTCGACTCCCTCAC 59.033 55.000 17.92 0.00 0.00 3.51
611 624 0.388649 CCTTTGTCGACTCCCTCACG 60.389 60.000 17.92 0.00 0.00 4.35
612 625 1.006571 TTTGTCGACTCCCTCACGC 60.007 57.895 17.92 0.00 0.00 5.34
613 626 1.461091 TTTGTCGACTCCCTCACGCT 61.461 55.000 17.92 0.00 0.00 5.07
616 629 3.125573 CGACTCCCTCACGCTCGA 61.126 66.667 0.00 0.00 0.00 4.04
618 631 3.053849 GACTCCCTCACGCTCGACC 62.054 68.421 0.00 0.00 0.00 4.79
619 632 3.827898 CTCCCTCACGCTCGACCC 61.828 72.222 0.00 0.00 0.00 4.46
1003 1031 6.494666 TGGAGGTGGAGTAGTATAAAATGG 57.505 41.667 0.00 0.00 0.00 3.16
1032 1087 3.030652 CAACTCGTTGGTGCACCC 58.969 61.111 32.62 17.38 36.95 4.61
1049 1104 3.282157 CGCAATGGATCAGGCCGG 61.282 66.667 0.00 0.00 0.00 6.13
1404 1459 3.430862 CCCACCCGCATGTTCACG 61.431 66.667 0.00 0.00 0.00 4.35
1621 1712 2.467826 GCCATGTTCGAGCTGCTCC 61.468 63.158 22.97 10.42 0.00 4.70
2042 2151 1.817209 CCAAGGTCTACGAGGAGGC 59.183 63.158 0.00 0.00 0.00 4.70
2543 2669 2.427453 TCATCGTCTCCAGAAGCTAACC 59.573 50.000 0.00 0.00 0.00 2.85
2556 2682 0.885196 GCTAACCATTTCCCACGCAA 59.115 50.000 0.00 0.00 0.00 4.85
2604 2730 3.476295 AGAATACGTCGACGCAACTTA 57.524 42.857 35.92 21.20 44.43 2.24
2709 4270 9.385902 CTATAAAAGATACATCAACATTTGCGG 57.614 33.333 0.00 0.00 0.00 5.69
2712 4273 3.443329 AGATACATCAACATTTGCGGCAA 59.557 39.130 12.11 12.11 0.00 4.52
2755 4320 2.112522 CAGTACAGATACAAGCGCTCG 58.887 52.381 12.06 0.00 33.30 5.03
2762 4327 6.250344 ACAGATACAAGCGCTCGTATATAA 57.750 37.500 20.49 0.00 0.00 0.98
2763 4328 6.084925 ACAGATACAAGCGCTCGTATATAAC 58.915 40.000 20.49 8.68 0.00 1.89
2779 4344 7.609632 CGTATATAACGTGCATACAATCATCC 58.390 38.462 12.33 0.00 46.72 3.51
2780 4345 7.274686 CGTATATAACGTGCATACAATCATCCA 59.725 37.037 12.33 0.00 46.72 3.41
2788 4353 6.073112 CGTGCATACAATCATCCATATGAACA 60.073 38.462 3.65 0.00 45.12 3.18
2790 4355 6.073112 TGCATACAATCATCCATATGAACACG 60.073 38.462 3.65 0.00 45.12 4.49
2791 4356 6.621380 GCATACAATCATCCATATGAACACGG 60.621 42.308 3.65 0.00 45.12 4.94
2792 4357 4.136796 ACAATCATCCATATGAACACGGG 58.863 43.478 3.65 0.00 45.12 5.28
2793 4358 4.141505 ACAATCATCCATATGAACACGGGA 60.142 41.667 3.65 0.00 45.12 5.14
2795 4360 3.804036 TCATCCATATGAACACGGGAAC 58.196 45.455 3.65 0.00 39.20 3.62
2799 4364 3.054728 TCCATATGAACACGGGAACACAT 60.055 43.478 3.65 0.00 0.00 3.21
2800 4365 3.065233 CCATATGAACACGGGAACACATG 59.935 47.826 3.65 0.00 0.00 3.21
2801 4366 0.881118 ATGAACACGGGAACACATGC 59.119 50.000 0.00 0.00 0.00 4.06
2802 4367 0.464554 TGAACACGGGAACACATGCA 60.465 50.000 0.00 0.00 0.00 3.96
2804 4369 1.781025 AACACGGGAACACATGCACG 61.781 55.000 0.00 0.00 0.00 5.34
2808 4389 0.869068 CGGGAACACATGCACGTTTA 59.131 50.000 0.00 0.00 0.00 2.01
2823 4404 1.360820 GTTTAAGAGACTGAGCCGGC 58.639 55.000 21.89 21.89 0.00 6.13
2824 4405 0.108804 TTTAAGAGACTGAGCCGGCG 60.109 55.000 23.20 9.91 0.00 6.46
2830 4411 3.501458 GACTGAGCCGGCGTATCCC 62.501 68.421 23.20 6.40 0.00 3.85
2833 4414 2.143594 CTGAGCCGGCGTATCCCTAC 62.144 65.000 23.20 5.81 0.00 3.18
2847 4428 4.920640 ATCCCTACGAATACACAGACAG 57.079 45.455 0.00 0.00 0.00 3.51
2884 4943 0.652071 GTCCGTCCAACGTCGTTTTT 59.348 50.000 8.15 0.00 40.58 1.94
2921 4980 8.345565 AGACTACGAATTTTGATCCAATAATGC 58.654 33.333 0.00 0.00 0.00 3.56
2949 5664 3.064271 GCGTCTCGAGTCTTCTATCAACT 59.936 47.826 13.13 0.00 0.00 3.16
2987 5835 8.196802 TGTAGACTACGAATTTTGATCCAATG 57.803 34.615 8.09 0.00 0.00 2.82
3011 5859 3.243301 TGTGTTTAGCGTCTCGAGTCTTT 60.243 43.478 13.13 0.41 0.00 2.52
3015 5863 6.089150 GTGTTTAGCGTCTCGAGTCTTTTATT 59.911 38.462 13.13 0.00 0.00 1.40
3016 5864 7.272084 GTGTTTAGCGTCTCGAGTCTTTTATTA 59.728 37.037 13.13 0.00 0.00 0.98
3017 5865 7.809331 TGTTTAGCGTCTCGAGTCTTTTATTAA 59.191 33.333 13.13 0.10 0.00 1.40
3199 6051 4.834892 CTCGCCGGGCATTTTGCG 62.835 66.667 20.71 2.82 46.21 4.85
3264 6116 9.814899 TGACACAAACAAGTTGATGAATAAAAT 57.185 25.926 10.54 0.00 39.87 1.82
3307 6159 4.895668 AAATCATGCCCACAAGTTCATT 57.104 36.364 0.00 0.00 0.00 2.57
3458 6310 0.242286 CTCCCTATCCTCATCACGCG 59.758 60.000 3.53 3.53 0.00 6.01
3459 6311 0.467474 TCCCTATCCTCATCACGCGT 60.467 55.000 5.58 5.58 0.00 6.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.621892 AAGAGGCGGCGTCGTGTAC 62.622 63.158 12.58 0.00 38.89 2.90
11 12 3.332493 GAAGAGGCGGCGTCGTGTA 62.332 63.158 12.58 0.00 38.89 2.90
12 13 4.719369 GAAGAGGCGGCGTCGTGT 62.719 66.667 12.58 6.12 38.89 4.49
22 23 4.400961 AGGCACGCAGGAAGAGGC 62.401 66.667 0.00 0.00 0.00 4.70
23 24 2.435586 CAGGCACGCAGGAAGAGG 60.436 66.667 0.00 0.00 0.00 3.69
24 25 2.031516 CACAGGCACGCAGGAAGAG 61.032 63.158 0.00 0.00 0.00 2.85
25 26 2.031012 CACAGGCACGCAGGAAGA 59.969 61.111 0.00 0.00 0.00 2.87
26 27 2.786539 TAGCACAGGCACGCAGGAAG 62.787 60.000 0.00 0.00 44.61 3.46
27 28 2.184020 ATAGCACAGGCACGCAGGAA 62.184 55.000 0.00 0.00 44.61 3.36
28 29 2.184020 AATAGCACAGGCACGCAGGA 62.184 55.000 0.00 0.00 44.61 3.86
29 30 0.461870 TAATAGCACAGGCACGCAGG 60.462 55.000 0.00 0.00 44.61 4.85
30 31 1.262417 CATAATAGCACAGGCACGCAG 59.738 52.381 0.00 0.00 44.61 5.18
31 32 1.298602 CATAATAGCACAGGCACGCA 58.701 50.000 0.00 0.00 44.61 5.24
32 33 1.299541 ACATAATAGCACAGGCACGC 58.700 50.000 0.00 0.00 44.61 5.34
33 34 2.677836 ACAACATAATAGCACAGGCACG 59.322 45.455 0.00 0.00 44.61 5.34
34 35 3.689161 TGACAACATAATAGCACAGGCAC 59.311 43.478 0.00 0.00 44.61 5.01
35 36 3.949132 TGACAACATAATAGCACAGGCA 58.051 40.909 0.00 0.00 44.61 4.75
36 37 5.180117 CCTATGACAACATAATAGCACAGGC 59.820 44.000 0.00 0.00 38.33 4.85
37 38 6.291377 ACCTATGACAACATAATAGCACAGG 58.709 40.000 0.00 0.00 38.33 4.00
38 39 7.792374 AACCTATGACAACATAATAGCACAG 57.208 36.000 0.00 0.00 38.33 3.66
39 40 8.261522 TGTAACCTATGACAACATAATAGCACA 58.738 33.333 0.00 0.00 38.33 4.57
40 41 8.548721 GTGTAACCTATGACAACATAATAGCAC 58.451 37.037 0.00 0.00 38.33 4.40
41 42 8.261522 TGTGTAACCTATGACAACATAATAGCA 58.738 33.333 0.00 0.00 35.07 3.49
42 43 8.657074 TGTGTAACCTATGACAACATAATAGC 57.343 34.615 0.00 0.00 35.07 2.97
43 44 9.817809 ACTGTGTAACCTATGACAACATAATAG 57.182 33.333 0.00 0.00 35.07 1.73
44 45 9.594478 CACTGTGTAACCTATGACAACATAATA 57.406 33.333 0.00 0.00 35.07 0.98
45 46 8.100791 ACACTGTGTAACCTATGACAACATAAT 58.899 33.333 12.53 0.00 35.07 1.28
46 47 7.446769 ACACTGTGTAACCTATGACAACATAA 58.553 34.615 12.53 0.00 35.07 1.90
47 48 6.999950 ACACTGTGTAACCTATGACAACATA 58.000 36.000 12.53 0.00 35.27 2.29
48 49 5.865085 ACACTGTGTAACCTATGACAACAT 58.135 37.500 12.53 0.00 36.89 2.71
49 50 5.284861 ACACTGTGTAACCTATGACAACA 57.715 39.130 12.53 0.00 34.36 3.33
50 51 7.321153 AGATACACTGTGTAACCTATGACAAC 58.679 38.462 23.03 0.00 36.31 3.32
51 52 7.476540 AGATACACTGTGTAACCTATGACAA 57.523 36.000 23.03 0.00 36.31 3.18
52 53 7.067859 GGTAGATACACTGTGTAACCTATGACA 59.932 40.741 23.03 6.83 36.31 3.58
53 54 7.424001 GGTAGATACACTGTGTAACCTATGAC 58.576 42.308 23.03 16.22 36.31 3.06
54 55 6.548622 GGGTAGATACACTGTGTAACCTATGA 59.451 42.308 26.98 12.25 36.31 2.15
55 56 6.550108 AGGGTAGATACACTGTGTAACCTATG 59.450 42.308 26.98 0.00 38.80 2.23
56 57 6.680540 AGGGTAGATACACTGTGTAACCTAT 58.319 40.000 26.98 18.54 38.80 2.57
57 58 6.069206 AGAGGGTAGATACACTGTGTAACCTA 60.069 42.308 26.98 23.51 40.72 3.08
58 59 4.944177 AGGGTAGATACACTGTGTAACCT 58.056 43.478 26.98 24.23 38.80 3.50
59 60 4.954826 AGAGGGTAGATACACTGTGTAACC 59.045 45.833 23.03 23.07 40.72 2.85
60 61 5.651139 TGAGAGGGTAGATACACTGTGTAAC 59.349 44.000 23.03 20.06 40.72 2.50
61 62 5.823312 TGAGAGGGTAGATACACTGTGTAA 58.177 41.667 23.03 5.78 40.72 2.41
62 63 5.446260 TGAGAGGGTAGATACACTGTGTA 57.554 43.478 21.68 21.68 40.72 2.90
63 64 4.317530 TGAGAGGGTAGATACACTGTGT 57.682 45.455 18.51 18.51 40.72 3.72
64 65 5.860941 ATTGAGAGGGTAGATACACTGTG 57.139 43.478 6.19 6.19 40.72 3.66
76 77 9.327731 CCTAGGTCTTTTATATATTGAGAGGGT 57.672 37.037 0.00 0.00 0.00 4.34
77 78 9.327731 ACCTAGGTCTTTTATATATTGAGAGGG 57.672 37.037 9.21 0.00 0.00 4.30
80 81 9.892444 TGGACCTAGGTCTTTTATATATTGAGA 57.108 33.333 35.12 4.19 44.04 3.27
82 83 9.892444 TCTGGACCTAGGTCTTTTATATATTGA 57.108 33.333 35.12 16.27 44.04 2.57
86 87 9.458727 CGTATCTGGACCTAGGTCTTTTATATA 57.541 37.037 35.12 21.76 44.04 0.86
87 88 8.168725 TCGTATCTGGACCTAGGTCTTTTATAT 58.831 37.037 35.12 22.58 44.04 0.86
88 89 7.520798 TCGTATCTGGACCTAGGTCTTTTATA 58.479 38.462 35.12 24.25 44.04 0.98
89 90 6.371278 TCGTATCTGGACCTAGGTCTTTTAT 58.629 40.000 35.12 25.08 44.04 1.40
90 91 5.759059 TCGTATCTGGACCTAGGTCTTTTA 58.241 41.667 35.12 21.12 44.04 1.52
91 92 4.607239 TCGTATCTGGACCTAGGTCTTTT 58.393 43.478 35.12 21.72 44.04 2.27
92 93 4.246712 TCGTATCTGGACCTAGGTCTTT 57.753 45.455 35.12 21.43 44.04 2.52
93 94 3.947612 TCGTATCTGGACCTAGGTCTT 57.052 47.619 35.12 21.73 44.04 3.01
94 95 3.553904 GTTCGTATCTGGACCTAGGTCT 58.446 50.000 35.12 21.31 44.04 3.85
95 96 2.622470 GGTTCGTATCTGGACCTAGGTC 59.378 54.545 30.72 30.72 43.87 3.85
96 97 2.664015 GGTTCGTATCTGGACCTAGGT 58.336 52.381 16.26 16.26 0.00 3.08
97 98 1.607628 CGGTTCGTATCTGGACCTAGG 59.392 57.143 7.41 7.41 0.00 3.02
98 99 1.607628 CCGGTTCGTATCTGGACCTAG 59.392 57.143 0.00 0.00 33.49 3.02
99 100 1.683943 CCGGTTCGTATCTGGACCTA 58.316 55.000 0.00 0.00 33.49 3.08
100 101 1.041447 CCCGGTTCGTATCTGGACCT 61.041 60.000 0.00 0.00 33.49 3.85
101 102 1.039233 TCCCGGTTCGTATCTGGACC 61.039 60.000 0.00 0.00 33.49 4.46
102 103 0.101939 GTCCCGGTTCGTATCTGGAC 59.898 60.000 0.00 0.34 33.49 4.02
103 104 1.039233 GGTCCCGGTTCGTATCTGGA 61.039 60.000 0.00 0.00 33.49 3.86
104 105 1.324740 TGGTCCCGGTTCGTATCTGG 61.325 60.000 0.00 0.00 0.00 3.86
105 106 0.533491 TTGGTCCCGGTTCGTATCTG 59.467 55.000 0.00 0.00 0.00 2.90
106 107 1.206371 CTTTGGTCCCGGTTCGTATCT 59.794 52.381 0.00 0.00 0.00 1.98
107 108 1.648504 CTTTGGTCCCGGTTCGTATC 58.351 55.000 0.00 0.00 0.00 2.24
108 109 0.251073 CCTTTGGTCCCGGTTCGTAT 59.749 55.000 0.00 0.00 0.00 3.06
109 110 1.672898 CCTTTGGTCCCGGTTCGTA 59.327 57.895 0.00 0.00 0.00 3.43
110 111 2.428622 CCTTTGGTCCCGGTTCGT 59.571 61.111 0.00 0.00 0.00 3.85
111 112 2.359478 CCCTTTGGTCCCGGTTCG 60.359 66.667 0.00 0.00 0.00 3.95
112 113 2.675423 GCCCTTTGGTCCCGGTTC 60.675 66.667 0.00 0.00 0.00 3.62
113 114 4.295199 GGCCCTTTGGTCCCGGTT 62.295 66.667 0.00 0.00 0.00 4.44
115 116 4.426313 GAGGCCCTTTGGTCCCGG 62.426 72.222 0.00 0.00 36.69 5.73
116 117 4.778143 CGAGGCCCTTTGGTCCCG 62.778 72.222 0.00 0.00 36.69 5.14
118 119 3.978571 GAGCGAGGCCCTTTGGTCC 62.979 68.421 0.00 0.00 36.69 4.46
119 120 2.436824 GAGCGAGGCCCTTTGGTC 60.437 66.667 0.00 0.00 36.05 4.02
120 121 4.035102 GGAGCGAGGCCCTTTGGT 62.035 66.667 0.00 0.00 0.00 3.67
121 122 3.721706 AGGAGCGAGGCCCTTTGG 61.722 66.667 0.00 0.00 0.00 3.28
122 123 2.437359 CAGGAGCGAGGCCCTTTG 60.437 66.667 0.00 0.00 29.31 2.77
123 124 3.721706 CCAGGAGCGAGGCCCTTT 61.722 66.667 0.00 0.00 29.31 3.11
133 134 1.006337 CATCTAGAGCGCCAGGAGC 60.006 63.158 7.17 7.17 38.52 4.70
134 135 0.313672 GTCATCTAGAGCGCCAGGAG 59.686 60.000 2.29 0.00 0.00 3.69
135 136 0.106469 AGTCATCTAGAGCGCCAGGA 60.106 55.000 2.29 0.00 0.00 3.86
136 137 0.313672 GAGTCATCTAGAGCGCCAGG 59.686 60.000 2.29 0.00 0.00 4.45
137 138 0.313672 GGAGTCATCTAGAGCGCCAG 59.686 60.000 2.29 0.00 0.00 4.85
138 139 0.395724 TGGAGTCATCTAGAGCGCCA 60.396 55.000 2.29 11.28 0.00 5.69
139 140 0.965439 ATGGAGTCATCTAGAGCGCC 59.035 55.000 2.29 3.30 0.00 6.53
140 141 3.441922 TGATATGGAGTCATCTAGAGCGC 59.558 47.826 0.00 0.00 34.96 5.92
141 142 5.125257 ACATGATATGGAGTCATCTAGAGCG 59.875 44.000 0.00 0.00 34.21 5.03
142 143 6.377996 AGACATGATATGGAGTCATCTAGAGC 59.622 42.308 0.00 0.00 34.21 4.09
143 144 7.943079 AGACATGATATGGAGTCATCTAGAG 57.057 40.000 0.00 0.00 34.21 2.43
144 145 8.386264 TGTAGACATGATATGGAGTCATCTAGA 58.614 37.037 0.00 0.00 34.21 2.43
145 146 8.458052 GTGTAGACATGATATGGAGTCATCTAG 58.542 40.741 0.00 0.00 34.21 2.43
146 147 7.944554 TGTGTAGACATGATATGGAGTCATCTA 59.055 37.037 0.00 0.00 34.21 1.98
147 148 6.779539 TGTGTAGACATGATATGGAGTCATCT 59.220 38.462 0.00 0.00 34.21 2.90
148 149 6.986250 TGTGTAGACATGATATGGAGTCATC 58.014 40.000 0.00 0.00 34.21 2.92
149 150 6.983906 TGTGTAGACATGATATGGAGTCAT 57.016 37.500 0.00 0.00 36.79 3.06
150 151 6.294176 CGATGTGTAGACATGATATGGAGTCA 60.294 42.308 10.71 0.00 43.22 3.41
151 152 6.089476 CGATGTGTAGACATGATATGGAGTC 58.911 44.000 10.71 0.00 43.22 3.36
152 153 5.536538 ACGATGTGTAGACATGATATGGAGT 59.463 40.000 10.71 0.00 43.22 3.85
153 154 6.018589 ACGATGTGTAGACATGATATGGAG 57.981 41.667 10.71 0.00 43.22 3.86
154 155 6.348213 CGTACGATGTGTAGACATGATATGGA 60.348 42.308 10.44 0.00 43.22 3.41
155 156 5.795441 CGTACGATGTGTAGACATGATATGG 59.205 44.000 10.44 0.00 43.22 2.74
156 157 6.599437 TCGTACGATGTGTAGACATGATATG 58.401 40.000 15.28 7.86 43.22 1.78
157 158 6.427242 ACTCGTACGATGTGTAGACATGATAT 59.573 38.462 19.87 0.00 43.22 1.63
158 159 5.756833 ACTCGTACGATGTGTAGACATGATA 59.243 40.000 19.87 0.00 43.22 2.15
159 160 4.575236 ACTCGTACGATGTGTAGACATGAT 59.425 41.667 19.87 0.68 43.22 2.45
160 161 3.937079 ACTCGTACGATGTGTAGACATGA 59.063 43.478 19.87 0.22 43.22 3.07
161 162 4.272480 GACTCGTACGATGTGTAGACATG 58.728 47.826 19.87 4.81 43.22 3.21
162 163 3.311871 GGACTCGTACGATGTGTAGACAT 59.688 47.826 19.87 4.97 46.01 3.06
163 164 2.674852 GGACTCGTACGATGTGTAGACA 59.325 50.000 19.87 0.00 36.22 3.41
164 165 2.674852 TGGACTCGTACGATGTGTAGAC 59.325 50.000 19.87 6.16 32.51 2.59
165 166 2.976589 TGGACTCGTACGATGTGTAGA 58.023 47.619 19.87 0.80 32.51 2.59
166 167 3.126514 ACTTGGACTCGTACGATGTGTAG 59.873 47.826 19.87 15.21 32.51 2.74
167 168 3.076621 ACTTGGACTCGTACGATGTGTA 58.923 45.455 19.87 7.33 0.00 2.90
168 169 1.884579 ACTTGGACTCGTACGATGTGT 59.115 47.619 19.87 13.50 0.00 3.72
169 170 2.516923 GACTTGGACTCGTACGATGTG 58.483 52.381 19.87 10.00 0.00 3.21
170 171 1.471684 GGACTTGGACTCGTACGATGT 59.528 52.381 19.87 17.95 0.00 3.06
171 172 1.471287 TGGACTTGGACTCGTACGATG 59.529 52.381 19.87 14.87 0.00 3.84
172 173 1.830279 TGGACTTGGACTCGTACGAT 58.170 50.000 19.87 9.13 0.00 3.73
173 174 1.608055 TTGGACTTGGACTCGTACGA 58.392 50.000 18.41 18.41 0.00 3.43
174 175 2.649331 ATTGGACTTGGACTCGTACG 57.351 50.000 9.53 9.53 0.00 3.67
175 176 3.660865 ACAATTGGACTTGGACTCGTAC 58.339 45.455 10.83 0.00 0.00 3.67
176 177 5.232463 GTTACAATTGGACTTGGACTCGTA 58.768 41.667 10.83 0.00 0.00 3.43
177 178 2.930826 ACAATTGGACTTGGACTCGT 57.069 45.000 10.83 0.00 0.00 4.18
178 179 3.435671 GGTTACAATTGGACTTGGACTCG 59.564 47.826 10.83 0.00 0.00 4.18
179 180 4.652822 AGGTTACAATTGGACTTGGACTC 58.347 43.478 10.83 0.00 0.00 3.36
180 181 4.724279 AGGTTACAATTGGACTTGGACT 57.276 40.909 10.83 0.00 0.00 3.85
181 182 6.415573 AGATAGGTTACAATTGGACTTGGAC 58.584 40.000 10.83 0.00 0.00 4.02
182 183 6.636454 AGATAGGTTACAATTGGACTTGGA 57.364 37.500 10.83 0.00 0.00 3.53
183 184 8.980481 ATAAGATAGGTTACAATTGGACTTGG 57.020 34.615 10.83 0.00 0.00 3.61
221 222 6.491714 ACCATCATCTGCTAGAGTTGTATT 57.508 37.500 0.00 0.00 0.00 1.89
223 224 5.395657 CCAACCATCATCTGCTAGAGTTGTA 60.396 44.000 0.00 0.00 33.27 2.41
233 234 1.825090 TGTGTCCAACCATCATCTGC 58.175 50.000 0.00 0.00 0.00 4.26
247 248 1.059264 GAGCGCGTTAAGTGATGTGTC 59.941 52.381 8.43 0.00 0.00 3.67
250 251 1.067846 TGAGAGCGCGTTAAGTGATGT 60.068 47.619 8.43 0.00 0.00 3.06
253 254 0.732880 GCTGAGAGCGCGTTAAGTGA 60.733 55.000 8.43 0.00 0.00 3.41
264 265 3.365767 GGTCATTTTTGTGAGCTGAGAGC 60.366 47.826 0.00 0.00 41.96 4.09
281 282 1.496060 TGGAGCATCGTAAGGGTCAT 58.504 50.000 0.00 0.00 34.37 3.06
307 308 6.430962 TGAGAGCAGCTGATTAAAGGATAT 57.569 37.500 20.43 0.00 0.00 1.63
322 323 8.910666 CGAGTATAAGTCATTTTATGAGAGCAG 58.089 37.037 0.00 0.00 40.53 4.24
388 395 2.263545 TGGATAGAGATGCATGGAGGG 58.736 52.381 2.46 0.00 0.00 4.30
393 400 4.907809 AGTTGGATGGATAGAGATGCATG 58.092 43.478 2.46 0.00 43.55 4.06
394 401 5.579753 AAGTTGGATGGATAGAGATGCAT 57.420 39.130 0.00 0.00 45.94 3.96
395 402 5.378230 AAAGTTGGATGGATAGAGATGCA 57.622 39.130 0.00 0.00 37.85 3.96
396 403 6.060788 AGAAAAGTTGGATGGATAGAGATGC 58.939 40.000 0.00 0.00 0.00 3.91
431 444 4.666655 CGTGAATGAAAACGAGGTGATGAC 60.667 45.833 0.00 0.00 42.32 3.06
432 445 3.431912 CGTGAATGAAAACGAGGTGATGA 59.568 43.478 0.00 0.00 42.32 2.92
434 447 3.399330 ACGTGAATGAAAACGAGGTGAT 58.601 40.909 1.80 0.00 42.32 3.06
435 448 2.828877 ACGTGAATGAAAACGAGGTGA 58.171 42.857 1.80 0.00 42.32 4.02
436 449 4.025563 TGTTACGTGAATGAAAACGAGGTG 60.026 41.667 0.00 0.00 42.32 4.00
437 450 4.121317 TGTTACGTGAATGAAAACGAGGT 58.879 39.130 0.00 0.00 42.32 3.85
438 451 4.718858 TGTTACGTGAATGAAAACGAGG 57.281 40.909 0.00 0.00 42.32 4.63
439 452 7.406832 CGATTTTGTTACGTGAATGAAAACGAG 60.407 37.037 0.00 0.00 42.32 4.18
440 453 6.354883 CGATTTTGTTACGTGAATGAAAACGA 59.645 34.615 0.00 0.00 42.32 3.85
441 454 6.493069 CGATTTTGTTACGTGAATGAAAACG 58.507 36.000 0.00 0.00 45.15 3.60
442 455 6.278861 GCGATTTTGTTACGTGAATGAAAAC 58.721 36.000 0.00 0.00 0.00 2.43
486 499 0.161024 GACGGAAGAGAAACGCAACG 59.839 55.000 0.00 0.00 0.00 4.10
489 502 0.249155 AACGACGGAAGAGAAACGCA 60.249 50.000 0.00 0.00 0.00 5.24
490 503 0.433871 GAACGACGGAAGAGAAACGC 59.566 55.000 0.00 0.00 0.00 4.84
491 504 1.450905 GTGAACGACGGAAGAGAAACG 59.549 52.381 0.00 0.00 0.00 3.60
492 505 2.218075 GTGTGAACGACGGAAGAGAAAC 59.782 50.000 0.00 0.00 0.00 2.78
560 573 3.244078 TGGAGAGAACAATAACACTGCGT 60.244 43.478 0.00 0.00 0.00 5.24
960 973 1.654954 GCGAGTTAGAGCGTGAGGGA 61.655 60.000 0.00 0.00 0.00 4.20
961 974 1.226717 GCGAGTTAGAGCGTGAGGG 60.227 63.158 0.00 0.00 0.00 4.30
962 975 0.524392 CAGCGAGTTAGAGCGTGAGG 60.524 60.000 0.00 0.00 38.61 3.86
963 976 0.524392 CCAGCGAGTTAGAGCGTGAG 60.524 60.000 0.00 0.00 38.61 3.51
964 977 0.958876 TCCAGCGAGTTAGAGCGTGA 60.959 55.000 0.00 0.00 38.61 4.35
965 978 0.524392 CTCCAGCGAGTTAGAGCGTG 60.524 60.000 0.00 0.00 38.61 5.34
966 979 1.658686 CCTCCAGCGAGTTAGAGCGT 61.659 60.000 0.00 0.00 38.61 5.07
967 980 1.064946 CCTCCAGCGAGTTAGAGCG 59.935 63.158 0.00 0.00 38.61 5.03
968 981 0.179124 CACCTCCAGCGAGTTAGAGC 60.179 60.000 0.00 0.00 33.93 4.09
1003 1031 1.507096 CGAGTTGCAACGTTAGCGC 60.507 57.895 23.21 0.00 42.83 5.92
1032 1087 3.282157 CCGGCCTGATCCATTGCG 61.282 66.667 0.00 0.00 0.00 4.85
1049 1104 1.331399 GGTGGAGGTGGAGTAGGAGC 61.331 65.000 0.00 0.00 0.00 4.70
1078 1133 3.077556 GGAGCCGAGGAGGAGCAA 61.078 66.667 0.00 0.00 45.00 3.91
1185 1240 0.737715 CGAACTTGGCGAGGAAGAGG 60.738 60.000 6.71 0.00 0.00 3.69
1390 1445 2.358247 GGACGTGAACATGCGGGT 60.358 61.111 0.00 0.00 0.00 5.28
1391 1446 3.487202 CGGACGTGAACATGCGGG 61.487 66.667 0.00 0.00 0.00 6.13
1621 1712 1.709760 CGCCGAAGCACATGTACAG 59.290 57.895 0.00 0.00 39.83 2.74
2042 2151 1.012841 GAGCTCTGGATTGGCTTTCG 58.987 55.000 6.43 0.00 36.37 3.46
2451 2577 1.846124 GTCCACCTTCACCCCCTCA 60.846 63.158 0.00 0.00 0.00 3.86
2459 2585 2.184020 CTCCGCCATGTCCACCTTCA 62.184 60.000 0.00 0.00 0.00 3.02
2518 2644 0.735471 CTTCTGGAGACGATGAGCGA 59.265 55.000 0.00 0.00 44.57 4.93
2556 2682 4.769688 TCATATGTCGAGAGGTTGCATTT 58.230 39.130 1.90 0.00 0.00 2.32
2691 4252 3.419264 TGCCGCAAATGTTGATGTATC 57.581 42.857 0.00 0.00 0.00 2.24
2697 4258 0.964700 TCCATTGCCGCAAATGTTGA 59.035 45.000 10.42 0.03 36.06 3.18
2727 4288 8.573885 AGCGCTTGTATCTGTACTGTATTAATA 58.426 33.333 2.64 0.00 0.00 0.98
2730 4291 6.387041 AGCGCTTGTATCTGTACTGTATTA 57.613 37.500 2.64 0.00 0.00 0.98
2732 4293 4.554919 CGAGCGCTTGTATCTGTACTGTAT 60.555 45.833 13.26 0.00 0.00 2.29
2740 4301 6.541754 GTTATATACGAGCGCTTGTATCTG 57.458 41.667 40.50 16.63 39.95 2.90
2755 4320 8.474006 TGGATGATTGTATGCACGTTATATAC 57.526 34.615 0.00 0.00 0.00 1.47
2762 4327 5.550290 TCATATGGATGATTGTATGCACGT 58.450 37.500 2.13 0.00 37.15 4.49
2763 4328 6.073112 TGTTCATATGGATGATTGTATGCACG 60.073 38.462 2.13 0.00 41.77 5.34
2764 4329 7.080099 GTGTTCATATGGATGATTGTATGCAC 58.920 38.462 2.13 0.00 41.77 4.57
2765 4330 6.073112 CGTGTTCATATGGATGATTGTATGCA 60.073 38.462 2.13 0.00 41.77 3.96
2773 4338 4.141505 TGTTCCCGTGTTCATATGGATGAT 60.142 41.667 2.13 0.00 41.77 2.45
2779 4344 3.487376 GCATGTGTTCCCGTGTTCATATG 60.487 47.826 0.00 0.00 34.30 1.78
2780 4345 2.682856 GCATGTGTTCCCGTGTTCATAT 59.317 45.455 0.00 0.00 0.00 1.78
2788 4353 1.098712 AAACGTGCATGTGTTCCCGT 61.099 50.000 13.39 0.00 0.00 5.28
2790 4355 2.550606 TCTTAAACGTGCATGTGTTCCC 59.449 45.455 13.39 0.00 0.00 3.97
2791 4356 3.496884 TCTCTTAAACGTGCATGTGTTCC 59.503 43.478 13.39 0.00 0.00 3.62
2792 4357 4.211374 AGTCTCTTAAACGTGCATGTGTTC 59.789 41.667 13.39 0.00 0.00 3.18
2793 4358 4.024893 CAGTCTCTTAAACGTGCATGTGTT 60.025 41.667 13.39 11.31 0.00 3.32
2795 4360 3.740832 TCAGTCTCTTAAACGTGCATGTG 59.259 43.478 13.39 0.00 0.00 3.21
2799 4364 2.404215 GCTCAGTCTCTTAAACGTGCA 58.596 47.619 0.00 0.00 0.00 4.57
2800 4365 1.727335 GGCTCAGTCTCTTAAACGTGC 59.273 52.381 0.00 0.00 0.00 5.34
2801 4366 1.986378 CGGCTCAGTCTCTTAAACGTG 59.014 52.381 0.00 0.00 0.00 4.49
2802 4367 1.067776 CCGGCTCAGTCTCTTAAACGT 60.068 52.381 0.00 0.00 0.00 3.99
2804 4369 1.360820 GCCGGCTCAGTCTCTTAAAC 58.639 55.000 22.15 0.00 0.00 2.01
2808 4389 1.038130 ATACGCCGGCTCAGTCTCTT 61.038 55.000 26.68 0.00 0.00 2.85
2823 4404 4.274214 TGTCTGTGTATTCGTAGGGATACG 59.726 45.833 8.89 1.50 44.11 3.06
2824 4405 5.530171 TCTGTCTGTGTATTCGTAGGGATAC 59.470 44.000 6.88 6.88 0.00 2.24
2899 4958 7.022055 ACGCATTATTGGATCAAAATTCGTA 57.978 32.000 0.00 0.00 30.37 3.43
2962 5677 8.038351 TCATTGGATCAAAATTCGTAGTCTACA 58.962 33.333 10.59 0.00 0.00 2.74
2963 5678 8.420374 TCATTGGATCAAAATTCGTAGTCTAC 57.580 34.615 0.00 0.00 0.00 2.59
2964 5679 9.045223 CATCATTGGATCAAAATTCGTAGTCTA 57.955 33.333 0.00 0.00 0.00 2.59
2965 5680 7.554118 ACATCATTGGATCAAAATTCGTAGTCT 59.446 33.333 0.00 0.00 0.00 3.24
2966 5681 7.641411 CACATCATTGGATCAAAATTCGTAGTC 59.359 37.037 0.00 0.00 0.00 2.59
2968 5683 7.475015 ACACATCATTGGATCAAAATTCGTAG 58.525 34.615 0.00 0.00 0.00 3.51
2969 5684 7.389803 ACACATCATTGGATCAAAATTCGTA 57.610 32.000 0.00 0.00 0.00 3.43
2987 5835 2.847133 GACTCGAGACGCTAAACACATC 59.153 50.000 21.68 0.00 0.00 3.06
3011 5859 7.435488 GCTGTTCGAGATGCTCTTAGTTAATAA 59.565 37.037 0.00 0.00 0.00 1.40
3015 5863 4.440250 GGCTGTTCGAGATGCTCTTAGTTA 60.440 45.833 5.78 0.00 0.00 2.24
3016 5864 3.516615 GCTGTTCGAGATGCTCTTAGTT 58.483 45.455 0.00 0.00 0.00 2.24
3017 5865 2.159170 GGCTGTTCGAGATGCTCTTAGT 60.159 50.000 5.78 0.00 0.00 2.24
3031 5879 3.235355 GCTATAGCGCGGCTGTTC 58.765 61.111 9.40 0.00 40.10 3.18
3264 6116 6.462552 TTTGATGAACTTGTGGACATGAAA 57.537 33.333 0.00 0.00 0.00 2.69
3271 6123 5.472148 GCATGATTTTGATGAACTTGTGGA 58.528 37.500 0.00 0.00 0.00 4.02
3307 6159 5.083533 AGTTTGCATTTGAACTTGGTTGA 57.916 34.783 0.00 0.00 32.43 3.18


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.